Justin Upton hit a three-run homer in the ninth to make it 7-3, and that became crucial when the Mets rallied against Kimbrel.

They scored twice off the hard-throwing right-hander, who loaded the bases with a two-out walk to Lucas Duda. That’s when Gonzalez went to the mound and lifted Kimbrel, who didn’t look happy about it. He waited for an extra moment or two before reluctantly handing over the ball.

Kimbrel has been slowed recently by shoulder discomfort. He left, and Walden retired Travis d’Arnaud on a grounder to secure his first save of the season and Atlanta’s seventh victory in eight games.

Gold Glove shortstop Andrelton Simmons was shading toward the hole and made a strong throw to get d’Arnaud.

Santana (2-0) allowed one run and struck out seven, giving the Braves their latest outstanding start. Despite several injuries in spring training, Atlanta’s rotation entered with a 1.47 ERA - best in the majors by nearly a full run.

David Wright, Daniel Murphy and Chris Young all had three hits for the Mets, held to one by Aaron Harang and two relievers in the series opener Friday night. Wright’s eighth-inning single off Luis Avilan was New York’s only safety in a 6-0 loss.

Bartolo Colon (1-3) gave up three runs in seven innings for the Mets. There was some question about whether a bad back would prevent him from pitching after he was hit hard in a 14-2 loss to the Angels on Sunday.

Young cut it to 4-2 with an RBI single in the eighth off Braves reliever David Carpenter. Duda made a bid for a three-run homer with a long drive that was caught on the warning track in right field.

A single by d’Arnaud brought the Mets within one, but Carpenter ended the inning by retiring Ruben Tejada on an easy grounder with runners at the corners.

Upton’s fifth homer came off Jose Valverde and followed an intentional walk to Freeman. Kimbrel then came on in a non-save situation.

Atlanta was trailing 1-0 with two outs in the third when Freeman fisted a soft bouncer between the mound and home plate. Colon appeared to be in no particular rush to pick it up - and then he threw wildly past first base as Freeman hustled down the line.

Two runners scored on Colon’s error, and Freeman was credited with an infield single. But replays showed the ball hit Freeman’s front foot before bounding onto the grass, so it should have been ruled foul.

Mets manager Terry Collins went to the mound, then walked over to plate umpire Eric Cooper. After a discussion, Cooper huddled with the other umpires and the play stood - without a look at the replay. Fair ball.

Collins could not challenge the call because only batted balls that “first land at or beyond the set positions of the first or third base umpire” are subject to video review for fair or foul, according to baseball’s replay rules. Since the ball rolled right in front of the plate, the Mets had no recourse.

Freeman doubled home a run in the fifth, and Upton scored on Daisuke Matsuzaka’s wild pitch in the eighth to make it 4-1.

Santana threw 20 straight strikes against the Mets to begin his Braves debut April 9, when he allowed three hits in eight shutout innings. This time, he walked his first batter. Eric Young Jr. stole second and scored when Wright singled through a drawn-in infield.

NOTES: Gonzalez visited MLB’s replay center in Manhattan on Saturday morning. He said he was told the Braves were the only team that had come in for a firsthand look. … LHP Mike Minor (left shoulder tendinitis) gave up two earned runs in six innings in a rehab start for Triple-A Gwinnett. He could come off the disabled list next week. … Braves RHP Gavin Floyd (Tommy John surgery) threw 80 pitches Friday night for Double-A Mississippi in his fourth rehab start. … Chris Young doubled in the fourth for his first hit with the Mets.